Whole Wheat Apple Cinnamon Muffins

Hearty, healthy, and satisfying whole wheat muffins filled with sweet apples and plenty of cinnamon spice!

whole wheat apple cinnamon muffins

With zero refined sugar, by the way. (!!!)

Yep, I went there. The streak of healthy goodness continues. And guess what? Kevin loved these muffins. Not for one little second realizing that hello… they’re (1) whole wheat, (2) filled with fruit, and (3) not with sugar.

But before I get to the muffins: is it just me or did this week crawl by at a turtle’s pace? Scratch that. More like a snail. Whatever its speed, let’s just all be thankful that the weekend is here and it’s time to warm up and lounge around with healthy apple cinnamon muffins on our plates.

Cold weather necessity right here! ↓

overhead image of whole wheat apple cinnamon muffins

As you’re probably aware, I don’t mess around when it comes to muffins. Especially when it comes to muffins of the healthy variety. Chocolate banana resembling brownies (seriously, have you tried them?), strawberry chocolate chip with shockingly low calorie count, and these skinny banana blueberry muffins that gain all sorts of buzz this time of year. Lightened-up muffins are the peanut butter to my jelly. Sprinkles to my birthday cake. Netflix marathons to my weekends. In short: I can’t live without ’em.

So let me show you a new way to make them, apple cinnamon style.

Today’s muffins are adapted from my simple morning glory muffins, which have all sorts of goodies packed inside like grated apple, grated carrot, raisins, nuts, etc. Thick: carrot cake, but lightened-up. For today’s apple cinnamon version, we’re leaving out the grated carrot and switching up a couple other ingredients. To keep them on the lighter side, I use a mix of applesauce and oil. This way the muffins keep their moist, rich texture but aren’t weighed down with fat. Sometimes I find that replacing all of the fat in muffin recipes results in a rubbery texture. I use melted coconut oil in these, but you can use canola or vegetable instead.

2 images of muffin batter in a glass bowl and muffin batter in a muffin pan

Other healthy superstars: whole wheat flour (yes to that!) and apples. The muffins get a lot of their flavor and sweetness from the grated apples, so I suggest using a sweeter variety. And, of course, a variety you love because you’ll taste a lot of apple. I use Pink Lady or Fuji.

Also inside: pure maple syrup. None of that breakfast syrup stuff! The real deal, for concentrated flavor. Maple syrup in muffins is my new thing. It replaces the need for refined sugar. They aren’t super sweet muffins so if you love the high sugar stuff, you’ll miss the sugar here. A lot of sweetness comes from the apple, so again– that’s why I urge you to use a sweeter variety.

We’ve also got lots of cinnamon, some allspice, and chopped pecans for all sorts of delicious spice and goodness.

whole wheat apple cinnamon muffins in a muffin pan

You know how whole wheat muffins taste completely uninteresting? You don’t even want to waste your time. Or your calories. That’s not the story here. With all those sweet apple pieces overflowing every bite, the purely magical maple syrup lingering, that robust allspice, the cinnamon swirling, and fat-cutting applesauce… there’s so much to love. In every single warm, snuggly, healthy, unrefined sugary, whole wheat bite. ♥ I just described these as snuggly. And I’m OK with that.

whole wheat apple cinnamon muffins

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3 images of whole wheat apple cinnamon muffins

Whole Wheat Apple Cinnamon Muffins

  • Author: Sally
  • Prep Time: 15 minutes
  • Cook Time: 24 minutes
  • Total Time: 40 minutes
  • Yield: 15 muffins
  • Category: Muffins
  • Method: Baking
  • Cuisine: American


These healthy, simple, and amazing whole wheat apple cinnamon muffins are made without refined sugar.


  • 2 cups (245g) whole wheat flour* (spoon & leveled)
  • 1 teaspoon baking soda
  • 1 teaspoon baking powder
  • 2 teaspoons ground cinnamon
  • 1/2 teaspoon allspice
  • 1/2 teaspoon salt
  • 1/2 cup (64g) chopped pecans*
  • 3 large eggs
  • 2/3 cup (160ml) pure maple syrup (not breakfast syrup, the real stuff)*
  • 1/3 cup (80ml) vegetable, canola oil, or melted coconut oil
  • 1/3 cup (60g) smooth unsweetened applesauce*
  • 1 and 1/2 teaspoons pure vanilla extract
  • 2 cups (240g) shredded/grated apple (about 2 apples)*


  1. Preheat oven to 425°F (218°C)6. Spray a 12-count muffin pan with nonstick spray or use cupcake liners. This recipe makes 15 muffins, so prepare a second muffin pan with 3 liners.
  2. In a large bowl, whisk the flour, baking soda, baking powder, cinnamon, allspice, salt, and pecans together until combined. Set aside. In a medium bowl, whisk the eggs, maple syrup, oil, applesauce, and vanilla together until combined. Pour the wet ingredients into the dry ingredients, stir a few times, then add the grated apple. Fold everything together gently just until combined and no flour pockets remain.
  3. Spoon the batter into liners, filling them all the way to the top. Bake for 5 minutes at 425 then, keeping the muffins in the oven, reduce the oven temperature to 350°F (177°C). Bake for an additional 18 minutes or until a toothpick inserted in the center comes out clean. The total time these muffins take in the oven is about 23-24 minutes, give or take. (For mini muffins, bake 11-14 minutes at 350°F (177°C).) Allow the muffins to cool for 5 minutes in the muffin pan, then transfer to a wire rack to continue cooling.
  4. Muffins stay fresh covered at room temperature for a few days, then transfer to the fridge for up to 1 week.


  1. Freezing Instructions: For longer storage, freeze muffins for up to 3 months. Allow to thaw overnight in the refrigerator, then bring to room temperature or warm up in the microwave if desired.
  2. Flour: 2 cups of white whole wheat, whole wheat pastry flour, or all-purpose flour work too.
  3. Pecans: Instead of pecans, try chopped walnuts or even sunflower seeds. Or leave out completely. If using the nuts, feel free to toast them for 10 minutes at 300°F (148°C).
  4. Sweetener: You can use honey for the maple syrup, but the flavor will be different. Maple works so well with the apple cinnamon!
  5. Applesauce: Instead of applesauce, use an extra 1/3 cup of oil.
  6. Apples: Use a sweeter variety of apple that you love. I’ve used Pink Lady and Fuji. Both fantastic in these.
  7. Why the Initial High Temperature? The hot burst of air will spring up the top of the muffin quickly, then the inside of the muffin can bake for the remainder of the time. This helps the muffins rise nice and tall.
  8. Nutrition Information: Using SparkRecipes calculator, these muffins come out to 184 calories, 8g fat, 25g carbs each.
  9. Adapted from Simple Morning Glory Muffins.

Keywords: apple cinnamon muffins, whole wheat apple muffins


  1. Hi Sally! If I want to make this recipe into mini muffin, can you help with the bake time and temperature? Should I still bake them under 425 for 5 minutes?

    1. Hi Kath! For mini muffins, bake 11-14 minutes at 350°F (177°C). Use a toothpick to test for doneness.

  2. What can i add to substitute for eggs?

    If i will add honey instead of applesauce how much quantity do i need yo add ?

  3. How long should I bake these in a jumbo muffin tin?

    1. Bake at 425°F for 5 minutes, then, keeping the muffins in the oven, reduce the oven temperature to 350°F (177°C) and continue to bake for 25-26 minutes until the tops are lightly golden brown and centers are set. Use a toothpick to test. Enjoy!

      1. Thanks Sally! Love these muffins, as they aren’t too sweet but just right with the maple syrup and apples.

      2. This recipe was super easy to follow and they came out great. Moist despite not having apple sauce and using wholewheat flour, this will now by my weekly mid-afternoon snack, thank you!

      3. I’m so happy you enjoyed them, Christine!

  4. Hi Sally
    Just made this recipe and subbed out one of the apples for grated carrots. Also, for the shredding/grating, I just blitzed everything in my Cuisinart. The muffins turned out DELICIOUS and you can hardly tell that they’re whole wheat. Thanks so much for sharing this recipe! I’m looking forward to using these to kick start my kid’s first week back in school. 🙂

  5. I made this for school breakfast meal prep for my daughter. Love them! So easy to make, not too sweet and they were a hit with the kids.

  6. These are so good! Not too sweet, nicely cinnamon-flavored, chock full of apples, and hearty without feeling stodgy. I used Honeycrisp apples, which I love for just about anything. I’m not normally a fan of nuts in baked goods, but I had some pecans so included them. They add a nice crunch. They turned out perfect, will definitely make again.

  7. Brenda Silverstein says:

    Hi Sally,
    What would you think about making this with carrots instead of apples?
    Thanks for everything!

    1. Carrots should work! Just be sure to shred your own large carrots and don’t use the bags of pre-shredded carrots sold in the store as they are much more dry.

  8. These muffins are amazing!

  9. Can I replace the eggs with flaxseeds?

    1. I haven’t tried these with an egg substitute, but let me know if you do!

  10. I made these this morning! They came out great. They almost tasted buttery despite being dairy free. I had purchased the wrong flour at the grocery store a few days ago (I got white all purpose flour with wheat germ instead of regular all purpose) so I figured this would be a good opportunity to use it. The only thing was that the muffins stuck to the liners. Not a big deal, but next time I will just grease the muffin pan so I don’t need cupcake liners at all.

  11. Do you peel the apples before you grate them?

    1. That’s up to– won’t make a difference in the recipe either way.

  12. I made these twice in one week! They are so tasty! One batch I just did shredded apples and the other I added chopped walnuts and used 1/2 C honey in place of the maple syrup. They are in the freezer for quick breakfasts! Thank you so much for the recipe.

  13. How would you bake these as mini muffins? Is there a way to get a dome top if they are baked as mini muffins?

    1. For mini muffins, bake 11-14 minutes at 350°F (177°C). They are so small that the tops should still rise nicely!

      1. Jodi McGregor says:

        Thank you. I am going to make these as mini muffins for my daughter’s preschool class this week. It’s our week to bring snack, and I think they will be a healthy hit. Anything. but. goldfish.

  14. Just made these on a cold January day.
    We love whole wheat recipes and all apple ones too. They made 12 large muffins.
    Moist muffins. Felt disappointed that we could not taste any maple syrup. Especially at the price of maple syrup. Followed the recipe exactly.

    1. Hi Jill! You’re right, these do not have a strong maple flavor– mostly apple cinnamon. The maple is used to sweeten the muffins. You can use honey instead or a granulated sugar, too. Thank you so much for trying the recipe!

  15. Wonderful muffins. I substituted 1 c of crushed pineapple for 1 c of shredded apples and it turned out great

    1. I’m so glad you enjoyed them, pineapple sounds delicious!

  16. This was a lovely recipe. I made some substitutions based on what I had at home but it still turned out great. Instead of maple, I used a mix of agave and honey. I didn’t have enough of either so I made sure the applesauce (homemade) was sweetened, by which I mean macerated in malibu and a teaspoon of coconut sugar. Also shredded apples and pears instead of just using apples.
    I’ll be making this again for sure. Thank you

  17. Jennifer Hughes says:

    I made these because I thought I had apples that needed to be used up. After getting started, I found I only had 1 apple. Darn! I made up the difference with grated carrot and added in some currants. Excellent. (Oh, I also used all oil as I didn’t have applesauce.)
    THank you for another great recipe.

  18. Hi! Sally. Just wondering why there’s no butter and milk in the ingredients , only oil? Is it Ok to use / add Milk and butter? Thank you.

    1. Hi Eve, I recommend following the recipe as written. Oil keeps the muffins moister than butter would.

  19. Made these muffins exactly as written (amazing I had all the ingredients!). These are delicious! I thought they might be a bit heavy or dry due to the whole wheat flour but not so. Moist and tender. Just sweet enough with just a hint of maple flavour. Perfect for breakfast or mid morning snack. Thanks Sally for another great recipe…this is a keeper!

  20. This recipe sounds delicious! I just wondered if I could substitute olive oil for vegetable oil? So anxious to make these!
    Thanks for your reply in advance!

    1. Hi Lana, Olive would change the taste to make them a bit more savory. I suggest sticking with vegetable, canola oil, or melted coconut oil.

  21. Jodi McGregor says:

    I would like to make this recipe for my 3 year old’s preschool class. I don’t think they can eat the large muffins and would prefer to make mini muffins. How long should I bake them?

    1. For mini muffins, bake 11-14 minutes at 350°F (177°C).

  22. These are some of our family favorites! I’ve been making them for YEARS! They are the only muffins my husband will eat. Quick question though- I doubled the recipe. Can I refrigerate the batter so I can continue making fresh ones or should I just make them and then freeze them?

    1. I’m so happy that your family enjoys them so much! I recommend baking the batter right away and freezing the baked muffins.

  23. due to the raging here in New York and had a ton of whole wheat flour. Was hungry for muffins. Looked up this recipe, made it with my 6-year-old and we all loved it. Best served toasted with butter. My son ate 3 muffins in one spray and I was cool with it.

  24. Hi. I’m so excited to make these but I did have a question: is there any substitution I can use for the oil (either butter, olive oil, milk, more applesauce, etc.)?

    1. Hi Holly, You can try melted butter but the muffins might not be quite as moist.

  25. Hi Sally,
    Have forgotten the count of your recipes that I have tried . From cake pops to cookies. Can I use this to bake cake instead of muffins as we are in lockdown in India and I am at my mom’s. So wha should be the ideal temperature and time for baking.

  26. Made this today – as a loaf instead of muffins. Didn’t have enough apples, so I added dried cranberries in food processor with apples. Substituted pumpkin pie spice for allspice and walnuts for pecans, then added some apple juice to insure it was moist. Baked 45 minutes – turned out perfect!

  27. I loved the shape and texture of these muffins, the only thing that I disliked a bit was the overwhelming maple taste. I like maple, but this was a bit much for me. However, it may have been that we used strong, dark maple syrup, which has a lot of maple taste. I think next time I would do just 1/3 cup maple syrup to reduce the sweetness and maple flavour. Also, I used 1 egg and 2 flax eggs, which worked really well. I’m trying to cut down on using actual eggs for baking since we’d have to shop all the time if we used a ton of eggs.

  28. I had some past-their-prime apples to use up and searched the web for an apple-based, whole wheat muffin and saw a link to this recipe. Thanks so much for sharing it – it’s absolutely delicious, and will be a regular treat in our household.

    It turned out really well even though I made a few substitutions: 1:1 homemade date paste for maple syrup; instead of 3 eggs, 2 eggs plus 1/8 cup liquid egg white; and more each of applesauce (100-gram single-serving containers were all my grocery store had – pandemic shopping!) and apple (I used two whole honeycrisp apples for a total of 382 grams of shredded apple). I figured the extra liquid from apples and applesauce would compensate for the thickness of the date paste, and wasn’t too far off; I baked them for an extra 9 minutes, and will probably bake the next batch for a further 5 beyond that.

    The extra apple and applesauce meant more batter, so I made 19 instead of 15 muffins.

    Thanks again!

  29. I added fresh chopped cranberries, a pinch of nutmeg, and cloves. Sprinkled coconut sugar on top before baking. Pretty freaking fantastic. Thanks!

  30. Hi, I only have 110g of wheat flour left, does it work if I reduce all other ingredients by half as well? Thanks in advance!

    1. Hi Charlene, Yes you can cut the recipe in half.

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